Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Acss2

Cell type

Cell type Class
Neural
Cell type
CAD
NA
NA

Attributes by original data submitter

Sample

source_name
undifferentiated CAD cells, ACSS2 ChIP
strain/background
C57BL/6
cell line
CAD
differentiation state
undifferentiated
chip antibody
anti-ACSS2 (CS) (Cell Signaling 3658, lot# 1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed as previously described (Shah, P.P. et al. 2013), except that chromatin was sheared to an average size of <500 bp using the Covaris S220 Ultrasonicator. Equal aliquots of sonicated chromatin from undifferentiated and differentiated CAD neurons were used per immunoprecipitation reaction, and 10% of the amount was saved as input. Immunoprecipitation was performed using protein A Dynabeads (Life Technologies). Sequencing libraries were prepared using NEBNext Ultra library preparation procedure, and then assessed for quality and quantity by BioAnalyzer (Agilent) and qPCR (Kapa Biosystems).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
45575798
Reads aligned (%)
86.3
Duplicates removed (%)
32.2
Number of peaks
1691 (qval < 1E-05)

mm9

Number of total reads
45575798
Reads aligned (%)
86.0
Duplicates removed (%)
32.1
Number of peaks
2086 (qval < 1E-05)

Base call quality data from DBCLS SRA